The paired immunoglobulin-like type 2 receptor alpha (PILRA) gene polymorphism rs1859788 reduces risk of Alzheimer’s Disease in men homozygous for the ApoE ε4 allele

Background The APOE gene has long been associated with Alzheimer Disease (AD) risk. Emerging research indicates that other genetic loci, including the paired immunoglobulin-like type 2 receptor alpha (PILRA) gene, may play a crucial role. In the current study we used UK Biobank data to assess the relationship between PILRA and AD. Methods We examined the PILRA polymorphism rs1859788, a single nucleotide missense variant, G > A, minor allele frequency 0.3. Single nucleotide polymorphism (SNP) data for rs429358 and rs7412 determined APOE isoform. We used PheWeb to perform a phenome wide association study (phewas) of rs1859788 and identify other conditions that might be related to both AD and rs1859788. Results In male subjects homozygous for ApoE isoform ε4/ε4, of the men without AD, 9.7% had AA genotype; of the men with AD, 1.8% had AA genotype. This difference was significant (p = 0.006, two tail Fisher exact test). In female subjects homozygous for ApoE isoform ε4/ε4, of the women without AD, 10.4% had AA genotype; of the women with AD 7.9% had AA genotype. This difference was not significant (p = 0.481). In subjects not homozygous for ApoE isoform ε4/ε4, the effect of PILRA genotype was not significant. A phewas of rs1859788 found an association with megaloblastic anemia. Conclusion We have confirmed the previously noted PILRA snp rs1859788 risk reduction of AD, as well as a PILRA link to the ApoE ε4 isoform that has been previously described. We are uncertain why the significant association is only with men who are homozygous for the ε4/ε4 isoform. A phewas indicated that PILRA SNP rs1859788 is associated with megaloblastic anemia, which may explain an observed association between AD and anemia. The identification of PILRA as a potential risk gene for Alzheimer’s disease underscores the complexity of the genetic landscape contributing to AD. Alongside APOE, PILRA may play a significant role in modulating key pathological processes such as neuroinflammation and amyloid-beta accumulation.


Introduction
Alzheimer's disease affects millions worldwide and poses a signi cant public health challenge.AD is characterized by progressive cognitive decline and neuropathological hallmarks, including amyloid-beta (Aβ) plaques and neuro brillary tangles.AD is a complex disease involving genetic, environmental, and lifestyle factors.The APOE gene has long been associated with AD risk.Emerging research indicates that other genetic loci, including the paired immunoglobulin-like type 2 receptor alpha (PILRA) gene, may play a crucial role.Understanding these genetic in uences is critical for developing targeted interventions and improving diagnostic accuracy.
The APOE gene, located on chromosome 19, encodes apolipoprotein E, a protein involved in lipid metabolism and neuronal repair.The ε4 allele of APOE signi cantly increases AD risk, while the ε2 allele is protective.PILRA, located on chromosome 7q21, encodes an inhibitory receptor expressed on myeloid cells.A common missense variant (G78R, rs1859788) of PILRA may be protective against AD [1].
In the current study we used UK Biobank data to assess the relationship between PILRA and AD.

Methods
The UK Biobank is a large prospective observational study comprising approximately 500,000 men and women (N = 229,134 men, N = 273,402 women), more than 90% white, aged 40-69 years at enrollment.Participants were recruited from across 22 centers located throughout England, Wales, and Scotland between 2006 and 2010 and continue to be longitudinally followed for capture of subsequent health events [2].UK Biobank has approval from the Northwest Multi-center Research Ethics Committee (MREC) to obtain and disseminate data and samples from the participants, and these ethical regulations cover the work in this study.Written informed consent was obtained from all participants.Details can be found at www.ukbiobank.ac.uk/ethics.Our UK Biobank application was approved as UKB project 57245 (S.L., P.H.R.).Our analysis included all subjects genotyped for PILRA in the UK Biobank database.
We examined the PILRA single nucleotide polymorphism (SNP) rs1859788, a single nucleotide missense variant, G > A, minor allele frequency 0.3.SNP data for rs429358 and rs7412 determined APOE isoform [3].We used PheWeb [4] to perform a phenome wide association study (phewas) of rs1859788 to identify other conditions that might be related to both AD and rs1859788.
Data processing was performed on Minerva, a Linux mainframe with Centos 7.6, at the Icahn School of Medicine at Mount Sinai.We used PLINK, a whole-genome association analysis toolset, to analyze the UKB chromosome les [5].Statistical analysis was done with SPSS 26.

Results
Table 1 displays demographics of 483,936 subjects in the study.
Table 2 displays analysis of 9754 subjects homozygous for ApoE isoform ε4/ε4, PILRA genotype (GG, AG, AA) versus AD (yes or no).Of the men without AD, 9.7% had AA genotype; of the men with AD, 1.8% had AA genotype.This difference was signi cant (p = 0.006, two tail Fisher exact test).Of the women without AD, 10.4% had AA genotype; of the women with AD 7.9% had AA genotype.This difference was not signi cant (p = 0.481).In subjects not homozygous for ApoE isoform ε4/ε4, the effect of PILRA genotype was not signi cant.
A phewas of rs1859788 found an association with megaloblastic anemia ( gure 1 and table 3).

Discussion
We have con rmed the previously noted PILRA SNP rs1859788 risk reduction of AD, as well as a PILRA link to the ApoE ε4 isoform that has been previously described [6].We are uncertain why the signi cant association is only with men who are homozygous for the ε4/ε4 isoform.
A phewas ( gure 1 and table 3) indicated that PILRA SNP rs1859788 is associated with megaloblastic anemia, which may explain an observed association between AD and anemia.In one study, individuals with anemia had a 41% increased risk of developing AD and a 34% increased risk of developing any kind of dementia compared to those without anemia [7].Another study found that people with AD were often anemic, though not iron de cient [8].However, pernicious anemia can present with confusion, di culty concentrating, memory loss, cognitive decline, and be mistaken for AD [9].
PILRA is a member of the paired immunoglobulin-like type 2 receptor family and plays a role in immune regulation.It is an inhibitory receptor that modulates immune responses by interacting with its ligands on the surface of other cells.Whole exome sequencing studies (WES) have identi ed PILRA as a potential risk gene for AD, although its exact mechanism in disease pathology remains to be fully elucidated [10].
Recent studies suggest that PILRA may in uence neuroin ammation, a key feature of AD.
Neuroin ammation is driven by the activation of glial cells, which release in ammatory cytokines that can exacerbate neuronal damage.PILRA may affect the regulation of these immune responses, potentially modulating the in ammatory environment in the AD brain.
People who have PILRA gene loss-of-function mutations such as rs1859788 are protected from AD. Microglia increase their metabolism and reduce in ammatory reactions in the absence of PILRA, thereby ameliorating AD.A PILRA antibody replicates these actions and may be therapeutic for AD [11].
The interplay between APOE and PILRA in AD is an emerging area of research.Both genes are involved in processes that are central to AD pathology, such as amyloid-beta metabolism and neuroin ammation.
PILRA may interact with APOE to in uence the in ammatory response to amyloid-beta accumulation.
PILRA could modulate the activation of glial cells in APOE ε4 carriers, affecting the severity of in ammation and subsequent neuronal damage.
Understanding the genetic interactions between PILRA and APOE may provide insights into the heterogeneity of AD and help identify novel therapeutic targets.Personalized medicine approaches could consider these genetic factors to develop targeted interventions aimed at modifying disease progression in individuals with speci c genetic pro les.

Conclusion
The identi cation of PILRA as a potential risk gene for Alzheimer's disease underscores the complexity of the genetic landscape contributing to AD. Alongside APOE, PILRA may play a signi cant role in modulating key pathological processes such as neuroin ammation and amyloid-beta accumulation.
Further research into the interactions between these genes and their contributions to AD pathophysiology will be crucial for developing new therapeutic strategies and improving our understanding of this devastating disease.

Declarations
Data Data available from UK Biobank after approved application Tables

Table 2
Analysis of 9754 subjects homozygous APOE ε4/ε4, PILRA genotype (GG, AG, AA) versus AD (yes or no).Of the men without AD, 9.7% had AA genotype; of the men with AD, 1.8% had AA genotype.This difference was signi cant (p = 0.006, two tail Fisher exact test).Of the women without AD, 10.4% had AA genotype; of the women with AD 7.9% had AA genotype.This difference was not signi cant (p = 0.481).